4 ms·

Show HN: Interactive Tree of Life

115 points by Lucent 1mo ago

Ptree consolidates of 11 taxonomic trees, both categorical like we used in school (plant, animalia) and phylogenetic (evolutionary descent), with instant crosswalk between them. Across those trees it overlays 41 visual properties (categorical and numerical) assembled from hundreds of biological traits and sources. Color the tree by habitat, nutrition, size, longevity, even see vertical range of birds and depth of fish visually. The backend is 800 GB of raw data distilled through a 9-step build process that reconciles and links all 11 trees along with hundreds of traits so every node in every tree gets all the properties. Every color and number presented retains and shows its provenance: original wording, citation, and license. The frontend uses a custom Miller column implementation with fold-away gutter, all composited animation (no frameworks, pure DOM mutation). Use +'s to try to confuse it by expanding many branches and it will fold them away and route edges around them. Made by the creator of ptable.com, a popular interactive periodic table website around since 1997.

deleted 1mo ago
[deleted]
takomora 1mo ago
Great design, very snappy. Fun to browse and learn about species I didn't know exist and see how species are related to each other.
rhaps0dy 1mo ago
Super cool! I just learned about 'incertae sedis' from here—though I think these things should at least be in their kingdom (e.g. Naldaviricetes are clearly viruses no?)
- Lucent 1mo ago
  Absolutely agree with the underlying UX point. "Incertae sedis" shouldn't leave you unable to tell what broad kind of organism you're looking at. I do filter structural junk per backbone, but only from evidence that backbone itself supplies: synonym/accepted status, "not-a-taxon", environmental, hidden, unplaced flags. I also insert neutral buckets such as "classes (no phylum)" where ranks are skipped, so thousands of taxa don't spill into one flat level. What I deliberately don't do is move a taxon to the parent that I think makes more biological sense. Ptree (Ptable gets the same kind of requests to classify metalloids) is downstream of academic taxonomic authorities operating under something like Wikipedia's "no original research" policy. It can expose disagreement among authorities, but it shouldn't quietly become another undocumented taxonomy. Naldaviricetes is a good example. It is unquestionably a class of viruses, but "Viruses" is not necessarily its formal kingdom. ICTV currently leaves it unassigned to a realm, kingdom, or phylum so Ptree's ICTV backbone places it directly beneath a display root called Viruses. NCBI places it beneath "Viruses incertae sedis," while GBIF supplies it without that viral higher lineage, producing the confusing placement you found.
Aardwolf 28d ago
Some of the mouse-overs don't seem to match, hovering over 'viruses' shows a raccoon, and hovering over 'lungfish' shows a bird eating a fish
- Lucent 28d ago
  The problem with rolling up 2.2 million species into 7 kingdoms is it surfaces data quality issues loudly. Ranking photos by popularity means one node mismatch in millions due to a homonym will send that up from 10 levels deep. As I find these, I'm trying to squash them. That raccoon you see is actually suffering from Morbillivirus Canine Distemper Virus and that photo is correctly attached to that virus, and that bird is indeed eating a lungfish. I actually do penalize outlier favorite counts for photos because they're often meme-ish. I may blacklist this so the 2nd most favorited lungfish can surface. There are a lot of detailed rules that score which photo you get based on aspect ratio, whether the subject is in captivity, alive, etc.
dang 28d ago
> Made by the creator of ptable.com, a popular interactive periodic table website around since 1997. Discussed a few times over the years! Interactive Periodic Table - https://news.ycombinator.com/item?id=27650576 https://news.ycombinator.com/item?id=27650576 - June 2021 (22 comments) Dynamic Periodic Table (2017) - https://news.ycombinator.com/item?id=20495105 https://news.ycombinator.com/item?id=20495105 - July 2019 (21 comments) Worlds Best Periodic Table - https://news.ycombinator.com/item?id=4378346 https://news.ycombinator.com/item?id=4378346 - Aug 2012 (5 comments) Dynamic Periodic Table - https://news.ycombinator.com/item?id=3199922 https://news.ycombinator.com/item?id=3199922 - Nov 2011 (20 comments) Dynamic/Interactive Periodic Table - https://news.ycombinator.com/item?id=1193431 https://news.ycombinator.com/item?id=1193431 - March 2010 (2 comments)
kmoser 28d ago
Tufte would love this interface; it packs a ton of info, but is easy to use and understand.
- kpil 28d ago
  The tree map folding is ingenious. I have never seen it. As a whole it's brilliant and humbling. Both the vastness and complexity of nature and biology on Earth, and also the absurd amount of work and human lifetime that has been spent on gathering the information. It's also a testament of the power of Wikipedia.
  - Lucent 28d ago
    The gutter fold is entirely custom and took a month to get right. Try a link like this to see how the lines fold around each other in the gutter so hierarchy is preserved. https://ptree.org/#GBIF/Nutrition/42&view=tree&tab=wiki&open=55,7920181,256,8349555,8089559,4307512 https://ptree.org/#GBIF/Nutrition/42&view=tree&tab=wiki&open... The project only exists thanks to thousands of scientists carefully cataloguing all this data and releasing it CC-BY. I am only the interface.
    - kpil 24d ago
      I spent 5 minutes just playing with the folding :-D
      - Lucent 23d ago
        You're in luck. I just moved a lot more motion to the compositor. Cladogram got a big upgrade too in speed. Most annoying bug is that Chromium will not allow any SVG on the compositor if your devicePixelRatio isn't 1, which is practcally nobody on a modern laptop.
culi 28d ago
Very cool. Perhaps you've seen OneZoom[0] already which is purely based on phylogenetic data sourced from Open Tree of Life. OTOL has been around for a long time. The project aggregates phylogenetic data from thousands of studies and creates a massive synthetic tree.[1] It's neat because anyone can contribute. If you find a study not represented in there you can contribute the newick tree/annotation for it. [0] https://www.onezoom.org/ https://www.onezoom.org/ [1] https://tree.opentreeoflife.org/opentree/argus/ottol@378964/Solanum-lycopersicum https://tree.opentreeoflife.org/opentree/argus/ottol@378964/...
- Lucent 28d ago
  OneZoom is a great museum piece. Very engaging visualization that invites large touchscreen interaction. Impressive code behind it too for pruning offscreen vectors so the zoom stays smooth. On desktop however, perhaps due to my age, it gives me a bit of gorilla arm. Thanks to open data, I offer the same node hierarchy of OTT, among 10 other backbones, but present it with 3 different (perhaps less dazzling) viewing mechanics switchable at the top: Icicle, which packs hierarchy into a fixed vertical height while allowing depth to stay horizontally reachable. Chronogram is the opposite, showing structure even 10 levels deep in a compact horizontal region, but at the expense of large vertical expansion. And Tree, the default, which is a compromise that can also show multiple winding paths simultaneously by folding them against the gutter. I also focus less on the tree itself and more on trait overlay and rolling up thousands or even millions of species into compact segments so you can get a feel for how many chordates lay eggs or how many spiders are carnivorous at a glance. https://ptree.org/#OTT https://ptree.org/#OTT
  - culi 28d ago
    Yes I saw the OTT tab after I left my comment. Mostly I wanted to take the opportunity to sing the praises of the OTT project ptree is a very cool project! I'm a believer in the idea of mixing phylogenetic trees and trait tables. In tomato breeding, there is a lot of attention paid to closely related species as they hybridize quite readily. Being able to represent the phylogenetic relationships alongside their traits, habitats, etc is an extremely useful data visualization strategy. I actually made a tool to automate making charts like these but I don't think it's mature enough to share yet Anyhow really great work on the project
ohyoutravel 28d ago
Love this. Also love that this is coming from someone with expertise who, based on comments below, takes quality seriously. Particularly cool when juxtaposed against one the other day “Any Human Ever” which was at first enthralling and joy-inducing, but upon deeper inspection was just a slop factory spreading misinformation across the internet.
- Lucent 28d ago
  This is the highest compliment, and I see why no other projects have tried to join all the different trees of life together or attach and reconcile traits. This was the majority of the project. However, the unique "roll-up" visualization of traits brought in an interesting method of self-correction. For example, if any other phyla than the obvious 4 showed up with a single egg-laying species, I went back to the drawing board to find out where that incorrect join introduced the error.
stared 28d ago
Nice! One thing I am missing is an easy „go up” a taxonomy group.
- Lucent 22d ago
  Good addition! I just added it.
intrasight 28d ago
Clicks on ipad only work 20% of the time
- Lucent 28d ago
  I reproduced this bug and will have a fix out in an hour.
jsphweid 28d ago
Neat potentially. But in "species or group" I typed homo sapiens and it loaded up that whole tree. I noticed that a sibling of human is "cumshot man." I searched this on Google and expectedly got porn results. Not sure why that shows up.
- Lucent 28d ago
  This is vernacular picked up from Wikimedia commons for Homo rhodesiensis and its WikiData. It could be vandalism. I'll post to the Talk: and if it reverts, I'll reingest that source. https://commons.wikimedia.org/wiki/Category:Homo_rhodesiensis https://commons.wikimedia.org/wiki/Category:Homo_rhodesiensi... https://www.wikidata.org/wiki/Q131464 https://www.wikidata.org/wiki/Q131464 Edit: Regardless, I pulled it from production immediately out of an abundance of caution.
MarkusQ 28d ago
Took me a minute to figure out why I got a picture of a tree[1] for haloarchaea. https://www.inaturalist.org/photos/660443931 https://www.inaturalist.org/photos/660443931
searay112023 28d ago
Very nice!
andsoitis 28d ago
Love the use of the mSpace user experience. https://www.researchgate.net/publication/37538009_mSpace_Exploring_The_Semantic_Web_A_Technical_Report_in_Support_of_the_mSpace_software_framework https://www.researchgate.net/publication/37538009_mSpace_Exp...
vladsiu 27d ago
[dead]
cik 27d ago
Thank you for sharing this. It's such a great example of how fun learning and the internet can be. It's downright refreshing when things don't have the same exact design as the rest of the universe, and take the time to teach something.
Decimator 27d ago
Thanks for sharing. Really nice way to learn about the relationships in the animal tree.
saastown 26d ago
Its pretty cool project. I just shared this in my family group and they love it.
rustysnail 26d ago
[dead]

115 points by Lucent 1mo ago

deleted 1mo ago

[deleted]

takomora 1mo ago

Great design, very snappy. Fun to browse and learn about species I didn't know exist and see how species are related to each other.

rhaps0dy 1mo ago

Super cool! I just learned about 'incertae sedis' from here—though I think these things should at least be in their kingdom (e.g. Naldaviricetes are clearly viruses no?)

Lucent 1mo ago
Absolutely agree with the underlying UX point. "Incertae sedis" shouldn't leave you unable to tell what broad kind of organism you're looking at. I do filter structural junk per backbone, but only from evidence that backbone itself supplies: synonym/accepted status, "not-a-taxon", environmental, hidden, unplaced flags. I also insert neutral buckets such as "classes (no phylum)" where ranks are skipped, so thousands of taxa don't spill into one flat level. What I deliberately don't do is move a taxon to the parent that I think makes more biological sense. Ptree (Ptable gets the same kind of requests to classify metalloids) is downstream of academic taxonomic authorities operating under something like Wikipedia's "no original research" policy. It can expose disagreement among authorities, but it shouldn't quietly become another undocumented taxonomy. Naldaviricetes is a good example. It is unquestionably a class of viruses, but "Viruses" is not necessarily its formal kingdom. ICTV currently leaves it unassigned to a realm, kingdom, or phylum so Ptree's ICTV backbone places it directly beneath a display root called Viruses. NCBI places it beneath "Viruses incertae sedis," while GBIF supplies it without that viral higher lineage, producing the confusing placement you found.

Aardwolf 28d ago

Some of the mouse-overs don't seem to match, hovering over 'viruses' shows a raccoon, and hovering over 'lungfish' shows a bird eating a fish

Lucent 28d ago
The problem with rolling up 2.2 million species into 7 kingdoms is it surfaces data quality issues loudly. Ranking photos by popularity means one node mismatch in millions due to a homonym will send that up from 10 levels deep. As I find these, I'm trying to squash them. That raccoon you see is actually suffering from Morbillivirus Canine Distemper Virus and that photo is correctly attached to that virus, and that bird is indeed eating a lungfish. I actually do penalize outlier favorite counts for photos because they're often meme-ish. I may blacklist this so the 2nd most favorited lungfish can surface. There are a lot of detailed rules that score which photo you get based on aspect ratio, whether the subject is in captivity, alive, etc.

dang 28d ago

> Made by the creator of ptable.com, a popular interactive periodic table website around since 1997. Discussed a few times over the years! Interactive Periodic Table - https://news.ycombinator.com/item?id=27650576 https://news.ycombinator.com/item?id=27650576 - June 2021 (22 comments) Dynamic Periodic Table (2017) - https://news.ycombinator.com/item?id=20495105 https://news.ycombinator.com/item?id=20495105 - July 2019 (21 comments) Worlds Best Periodic Table - https://news.ycombinator.com/item?id=4378346 https://news.ycombinator.com/item?id=4378346 - Aug 2012 (5 comments) Dynamic Periodic Table - https://news.ycombinator.com/item?id=3199922 https://news.ycombinator.com/item?id=3199922 - Nov 2011 (20 comments) Dynamic/Interactive Periodic Table - https://news.ycombinator.com/item?id=1193431 https://news.ycombinator.com/item?id=1193431 - March 2010 (2 comments)

kmoser 28d ago

Tufte would love this interface; it packs a ton of info, but is easy to use and understand.

kpil 28d ago
The tree map folding is ingenious. I have never seen it. As a whole it's brilliant and humbling. Both the vastness and complexity of nature and biology on Earth, and also the absurd amount of work and human lifetime that has been spent on gathering the information. It's also a testament of the power of Wikipedia.
- Lucent 28d ago
  The gutter fold is entirely custom and took a month to get right. Try a link like this to see how the lines fold around each other in the gutter so hierarchy is preserved. https://ptree.org/#GBIF/Nutrition/42&view=tree&tab=wiki&open=55,7920181,256,8349555,8089559,4307512 https://ptree.org/#GBIF/Nutrition/42&view=tree&tab=wiki&open... The project only exists thanks to thousands of scientists carefully cataloguing all this data and releasing it CC-BY. I am only the interface.
  - kpil 24d ago
    I spent 5 minutes just playing with the folding :-D
    - Lucent 23d ago
      You're in luck. I just moved a lot more motion to the compositor. Cladogram got a big upgrade too in speed. Most annoying bug is that Chromium will not allow any SVG on the compositor if your devicePixelRatio isn't 1, which is practcally nobody on a modern laptop.

culi 28d ago

Very cool. Perhaps you've seen OneZoom[0] already which is purely based on phylogenetic data sourced from Open Tree of Life. OTOL has been around for a long time. The project aggregates phylogenetic data from thousands of studies and creates a massive synthetic tree.[1] It's neat because anyone can contribute. If you find a study not represented in there you can contribute the newick tree/annotation for it. [0] https://www.onezoom.org/ https://www.onezoom.org/ [1] https://tree.opentreeoflife.org/opentree/argus/ottol@378964/Solanum-lycopersicum https://tree.opentreeoflife.org/opentree/argus/ottol@378964/...

Lucent 28d ago
OneZoom is a great museum piece. Very engaging visualization that invites large touchscreen interaction. Impressive code behind it too for pruning offscreen vectors so the zoom stays smooth. On desktop however, perhaps due to my age, it gives me a bit of gorilla arm. Thanks to open data, I offer the same node hierarchy of OTT, among 10 other backbones, but present it with 3 different (perhaps less dazzling) viewing mechanics switchable at the top: Icicle, which packs hierarchy into a fixed vertical height while allowing depth to stay horizontally reachable. Chronogram is the opposite, showing structure even 10 levels deep in a compact horizontal region, but at the expense of large vertical expansion. And Tree, the default, which is a compromise that can also show multiple winding paths simultaneously by folding them against the gutter. I also focus less on the tree itself and more on trait overlay and rolling up thousands or even millions of species into compact segments so you can get a feel for how many chordates lay eggs or how many spiders are carnivorous at a glance. https://ptree.org/#OTT https://ptree.org/#OTT
- culi 28d ago
  Yes I saw the OTT tab after I left my comment. Mostly I wanted to take the opportunity to sing the praises of the OTT project ptree is a very cool project! I'm a believer in the idea of mixing phylogenetic trees and trait tables. In tomato breeding, there is a lot of attention paid to closely related species as they hybridize quite readily. Being able to represent the phylogenetic relationships alongside their traits, habitats, etc is an extremely useful data visualization strategy. I actually made a tool to automate making charts like these but I don't think it's mature enough to share yet Anyhow really great work on the project

ohyoutravel 28d ago

Love this. Also love that this is coming from someone with expertise who, based on comments below, takes quality seriously. Particularly cool when juxtaposed against one the other day “Any Human Ever” which was at first enthralling and joy-inducing, but upon deeper inspection was just a slop factory spreading misinformation across the internet.

Lucent 28d ago
This is the highest compliment, and I see why no other projects have tried to join all the different trees of life together or attach and reconcile traits. This was the majority of the project. However, the unique "roll-up" visualization of traits brought in an interesting method of self-correction. For example, if any other phyla than the obvious 4 showed up with a single egg-laying species, I went back to the drawing board to find out where that incorrect join introduced the error.

stared 28d ago

Nice! One thing I am missing is an easy „go up” a taxonomy group.

Lucent 22d ago
Good addition! I just added it.

intrasight 28d ago

Clicks on ipad only work 20% of the time

Lucent 28d ago
I reproduced this bug and will have a fix out in an hour.

jsphweid 28d ago

Neat potentially. But in "species or group" I typed homo sapiens and it loaded up that whole tree. I noticed that a sibling of human is "cumshot man." I searched this on Google and expectedly got porn results. Not sure why that shows up.

Lucent 28d ago
This is vernacular picked up from Wikimedia commons for Homo rhodesiensis and its WikiData. It could be vandalism. I'll post to the Talk: and if it reverts, I'll reingest that source. https://commons.wikimedia.org/wiki/Category:Homo_rhodesiensis https://commons.wikimedia.org/wiki/Category:Homo_rhodesiensi... https://www.wikidata.org/wiki/Q131464 https://www.wikidata.org/wiki/Q131464 Edit: Regardless, I pulled it from production immediately out of an abundance of caution.

MarkusQ 28d ago

Took me a minute to figure out why I got a picture of a tree[1] for haloarchaea. https://www.inaturalist.org/photos/660443931 https://www.inaturalist.org/photos/660443931

searay112023 28d ago

Very nice!

andsoitis 28d ago

Love the use of the mSpace user experience. https://www.researchgate.net/publication/37538009_mSpace_Exploring_The_Semantic_Web_A_Technical_Report_in_Support_of_the_mSpace_software_framework https://www.researchgate.net/publication/37538009_mSpace_Exp...

vladsiu 27d ago

[dead]

cik 27d ago

Thank you for sharing this. It's such a great example of how fun learning and the internet can be. It's downright refreshing when things don't have the same exact design as the rest of the universe, and take the time to teach something.

Decimator 27d ago

Thanks for sharing. Really nice way to learn about the relationships in the animal tree.

saastown 26d ago

Its pretty cool project. I just shared this in my family group and they love it.

rustysnail 26d ago

[dead]